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pharmaclaw-cheminformatics

Generate 3D conformers, map pharmacophores, fragment molecules, enumerate stereoisomers, and convert formats.

Updated Apr 9, 2026
Search Tags:#recap#conformers#format-conversion#library-design#pharmacophore#stereoisomers#rdkit-pypi
One-click install
npx skills add https://github.com/jakechen1/echo-research-framework --skill pharmaclaw-cheminformatics
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pharmaclaw-cheminformatics
Source: https://github.com/jakechen1/echo-research-framework/tree/main/skills-available/pharmaclaw-cheminformatics
Command: npx skills add https://github.com/jakechen1/echo-research-framework --skill pharmaclaw-cheminformatics

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires rdkit-pypi, Pillow, numpy, and includes scripts (resource) components.

What problem does it solve?

Advanced cheminformatics workflows for analyzing molecular structures in 3D, enabling conformer generation, pharmacophore mapping, RECAP fragmentation, stereoisomer enumeration, and robust format conversions to accelerate drug discovery and library design.

Core Features & Use Cases

  • 3D conformer generation and optimization for drug-like molecules (ETKDG with MMFF/UFF) to support docking and property prediction.
  • Pharmacophore mapping, fingerprints, and feature analysis for ADME profiling and scaffold design.
  • RECAP fragmentation with leaf/tree analysis to identify building blocks and shared scaffolds for library design.
  • Stereoisomer enumeration and analysis to characterize all possible configurations for lead optimization and patent planning.
  • Flexible format interconversion between SMILES, SDF, MOL, InChI/InChIKey, PDB, and XYZ for cross-tool interoperability.
  • End-to-end workflow via a chain entry that combines conformers, pharmacophore, recap, stereoisomers, and formats to produce a comprehensive molecular profile.

Quick Start

Input a SMILES string and chain through conformer generation, pharmacophore mapping, and format conversions to obtain a complete cheminformatics profile.

Frequently Asked Questions about pharmaclaw-cheminformatics

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I generate 3D conformers from SMILES for docking preparation?▼

You can generate 3D conformers from SMILES using ETKDG with MMFF or UFF optimization to produce drug-like molecular structures suitable for docking and property prediction.

Can I convert molecular formats between SDF, MOL, PDB, and SMILES?▼

Yes, you can convert molecular formats between SMILES, SDF, MOL, InChI/InChIKey, PDB, and XYZ to ensure cross-tool interoperability for your cheminformatics workflows.

How does RECAP fragmentation work for library design?▼

RECAP fragmentation breaks molecules into leaf and tree structures to identify shared scaffolds and building blocks, accelerating library design and patent planning workflows.

Do I need RDKit installed to enumerate stereoisomers and map pharmacophores?▼

Yes, you need Python 3.10+ and the rdkit-pypi package installed to enumerate stereoisomers, map pharmacophores, and execute the included cheminformatics scripts.

What is pharmacophore mapping used for in lead optimization?▼

Pharmacophore mapping identifies molecular features and fingerprints for ADME profiling and scaffold design, guiding lead optimization decisions during drug discovery.

Can I run an end-to-end cheminformatics workflow from a single SMILES input?▼

Yes, input a SMILES string and chain conformer generation, pharmacophore mapping, and format conversions to produce a comprehensive molecular profile for drug discovery.

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